Mechanobiology Institute& Department of Biological Sciences,
|Link to book|
Summary: Mechanical signals from the extracellular matrix impinge on cellular geometry resulting in altered functional nuclear landscape and gene expression programs. These alterations regulate diverse biological processes including stem-cell differentiation, developmental genetic programs and cellular homeostatic control systems. How such signals are integrated to the 3D spatio-temporal organization of the cell nucleus to elicit differential gene expression patterns are poorly understood. To investigate the biophysical principles underlying these processes, we use a multi-disciplinary approach, combining high resolution imaging of live-cells cultured on micro-patterned substrates, single-cell mechanics and genomics. In these projects, we engage in a number of collaborations with both theoretical and experimental groups. Our ongoing work is beginning to provide quantitative and modular links between cell geometry and nuclear mechanics in regulating 3D chromosome organization and genetic information.
G.V.Shivashankar, Annual Reviews of Biophysics, (2011), Vol.40, 361-378
G.V.Shivashankar, Editor, Methods in Cell Biology series, Elsevier Press
A brief description of ongoing projects is outlined below:
Project-1: Structural transitions in nuclear plasticity during stem-cell differentiation:
Stem cells are characterized by a highly plastic nucleus with bivalent histone modifications and an active transcriptome. Cellular differentiation programs, induced by physico-chemical signals, result in an increase in cytoplasmic-nuclear ratio, a prestressed nuclear architecture and non-random chromosome organization. However the mechanisms underlying the structural transitions in nuclear plasticity leading to cell-type specific transcription programs are unclear. In this project, we mapped the transitions in chromatin compaction states and the emergence of prestressed nuclear organization using mouse embryonic stem-cells cultured on micro-patterned substrates. Our experiments uncovered an unusual heterogeneity in chromatin assembly and its remodeling. This was also observed during early Drosophila embryogenesis and T-cell differentiation. These results suggest that such structural transitions in nuclear plasticity are generic and critical modulators of gene expression during differentiation and development.
Mechanical force alters morphogenetic movements and segmental gene expression patterns during Drosophila embryogenesis Abhishek Kumar & G.V. Shivashankar PLoS One. (2012) 7(3):e33089
Developmental heterogeneity in DNA packaging patterns influences T-cell activation and transmigration Soumya Gupta, Shefali Talwar, R.Indulaxmi, Lakshmi R. Perumalsamy, Apurva Sarin & G.V.Shivashankar PLoS One. (2012) 7(9):e43718
Probing Chromatin Structure and Dynamics Using Fluorescence Anisotropy Imaging, Ekta Makhija, K. Venkatesan Iyer, Shefali Talwar & G.V.Shivashankar (2013 - under review)
Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells, Shefali Talwar, Abhishek Kumar, Madan Rao, Gautam Menon and G.V.Shivashankar Biophysical Journal (2013) 104:553-64
Spatial compartmentalization of transcription control is dependent on nuclear mechanical heterogeneity during stem-cell differentiation, Shefali Talwar & G.V.Shivashankar (2013 - under review)
Project-2: Coupling between 3D nuclear organization and transcription control
Extracellular matrix signals are integrated to promoter sites, where active recruitment of transcription machinery results in altered gene expression. However the spatio-temporal dynamics underlying such transcription control is unclear. We show that the 3D organization of chromosome positions was sensitive to global transcription. In addition, within these inter-chromosome territories, the eukaryotic transcription machinery was found to be dynamic. Further, mechanical activation of cells resulted in chromatin remodeling preceding the nuclear mechanotransduction of transcription co-factors. Taken together our results suggest that the relative chromosome positions within the 3D architecture of the nucleus may be a major regulator of transcription control; integrating both transcription factors and transcription machinery.
- Dynamic organization of transcription factories is dependent on functional nuclear architecture Shovamayee Maharana, Divya Sharma, Shi Xianke & G.V. Shivashankar Biophysical Journal (2012) 103:851-859
- Dynamics of passive and active particles in the cell nucleus Feroz Meeran, Madan Rao & G.V.Shivashankar PLoS One. (2012) 7(10):e45843.
- Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes K.Venkatesan Iyer, Shovamayee Maharana, Soumya Gupta, Albert Libchaber, Tsvi Tlusty & G.V. Shivashankar PLoS One. (2012) 7(10):e46628. (Faculty of 1000 publication)
- Mechanical activation of cells reveals distinct timescales in chromatin remodeling
and MKL nuclear transport Venkatesan Iyer, Stephanie Pulford, Alex Mogilner and G.V.Shivashankar Biophysical Journal (2012) 103:1416-1428
Project-3: Impact of cellular geometry on nuclear mechanics and genome regulation
Cellular differentiation programs in physiology result in distinct cell shapes and nuclear morphology impinging on their function. In addition, depending on cell adhesion, cytoplasmic-nuclear links stabilize prestressed nuclear organization. This prestressed nuclear organization, determined by cell-geometric constraints, could serve as a substrate to integrate physico-chemical signals to the nucleus to regulate gene expression. However, the role of distinct cellular geometry in determining the physico-chemical coupling to the nucleus is unclear. Here we used micro-patterned substrates to alter cellular geometry (shape, aspect ratio and size) and study the nuclear homeostatic balance and the mechanotransduction pathways to regulate gene expression. Perinuclear actin organization was sensitive to cell-geometric constraints leading to actin-flow dependent nuclear rotational dynamics. In addition, genome-wide transcriptome analysis revealed cell geometry dependent alterations in actin related gene expression. Importantly, increase in area of cell-substrate interactions reinforced expression of matrix related genes while reduced cell-substrate area resulted in up-regulation of genes involved in cellular homeostasis. Taken together, our work suggests modularity in switching gene expression patterns by cell geometric constraints.
Role of actin dependent nuclear deformation in regulating early gene expression, Soumya Gupta, Nimi Marcel, Apurva Sarin and G.V.Shivashankar PLoS-One. (2012) 7(12):e53031
Acto-myosin contractility rotates the cell nucleus Abhishek Kumar, Ananyo Maitra, Madhuresh Sumit, Sriram Ramaswamy & G.V. Shivashankar (2013 - under review)
Cellular geometry regulate apical actin to nuclear coupling via direct contact with focal adhesion Li Qingsen, Abhishek Kumar, Ekta Makhija & G.V.Shivashankar (2013 - under review)
Cytoskeletal control of co-ordinated nuclear morphology and chromatin dynamics, Nisha Ramdas & G.V.Shivashankar (2013 - under review)
Model for deformation of cell nucleus by cortical actin layer Gur Fabrikanth, Soumya Gupta, G.V.Shivashankar & Misha Kozlov Biophysical Journal (2013-in press)
Cell geometric constraints differentially alter cytoplasmic to nuclear signaling to regulate gene expression Nikhil Jain, K.Venkatesan Iyer & G.V.Shivashankar Proceedings of the National Academy of Sciences-USA (2013) 110: 11349-54
Group members (updated September - 2013):
Phd students: Ekta Makhija, Nisha Ramdas, Yejun Wang
Postdoctoral Fellows: Toh Kee Chua, Li Qingsen, Radhakrishnan
Research Associate: Mallika Nagarjan
Research Assistant: Doorgesh Sharma Jokhun
Joint PhD students: Nikhil Jain (with Matsudaira lab), Aneesh Sathe (with Sheetz lab), Mrinal Shah (with Kenney lab), Xiaowei Shao (with Bershadsky lab)
Recent PhD students graduated from the lab in 2013:
Abhishek Kumar (Postdoctoral Fellow, Yale University)
Venkatesan Iyer (Postdoctoral Fellow, Max-Plank Institute, CBG, Dresden)
Shovamayee Maharana (Postdoctoral Fellow, Max-Plank Institute, CBG, Dresden)